Recent advances in stem cell biology provide a unique opportunity for researchers to investigate the molecular mechanisms underlying developmental diseases of the nervous system in living neurons derived from the cells of the affected subject. Several laboratories around the world are generating induced pluripotent stem (iPS) cell lines from hundreds of individuals with neurodegenerative and psychiatric disease. In some cases the subject has a known causal genetic mutation, while others express genetic risk alleles, and still others have no known genetic predisposition. While iPS cell technology provides an exciting inroad to study the effects of genetic alterations in the cells of interest, the field is in need of high throughput assays that allow for the analyses of effects in neuronal and glial subpopulations. Advances in nanotechnologies have provided a method to analyze single cells in a high throughput manner. Powerful assays have been developed using microengraving and single cell culture for the study of cells of the immune system. While the development of a similar method for neural cells presents unique challenges, successful profiling of individual neuronal and glial subtypes would allow researchers to interrogate gene function and dysfunction in specific cell types, and aid in the identification of the cell types most affected by specific genetic changes. Here, we propose to optimize a system to establish protein expression profiles for individual cell subtypes of the cerebral cortex over developmental time via real-time capture of secreted analytes, multiplexed immunostaining, and mass spectrometry imaging. In addition, we will investigate the identity of iPS cells differentiated to neuronal and glial cell fates, and determine the feasibility of using this system to determine effects of gene changes between iPS lines.